Evaluating and automating the annotation of a learner corpus

The paper describes a corpus of texts produced by non-native speakers of Czech. We discuss its annotation scheme, consisting of three interlinked tiers, designed to handle a wide range of error types present in the input. Each tier corrects different types of errors; links between the tiers allow capturing errors in word order and complex discontinuous expressions. Errors are not only corrected, but also classified. The annotation scheme is tested on a data set including approx. 175,000 words with fair inter-annotator agreement results. We also explore the possibility of applying automated linguistic annotation tools (taggers, spell checkers and grammar checkers) to the learner text to support or even substitute manual annotation.     

Neurogenesis as a Tool for Spinal Cord Injury

Spinal cord injury is a devastating medical condition with no effective treatment. One approach to SCI treatment may be provided by stem cells (SCs). Studies have mainly focused on the transplantation of exogenous SCs, but the induction of endogenous SCs has also been considered as an alternative. While the differentiation potential of neural stem cells in the brain neurogenic regions has been known for decades, there are ongoing debates regarding the multipotent differentiation potential of the ependymal cells of the central canal in the spinal cord (SCECs). Following spinal cord insult, SCECs start to proliferate and differentiate mostly into astrocytes and partly into oligodendrocytes, but not into neurons. However, there are several approaches concerning how to increase neurogenesis in the injured spinal cord, which are discussed in this review. The potential treatment approaches include drug administration, the reduction of neuroinflammation, neuromodulation with physical factors and in vivo reprogramming.     

Matrix Metalloproteinases and Their Role in Mechanisms Underlying Effects of Quercetin on Heart Function in Aged Zucker Diabetic Fatty Rats

Several mechanisms may contribute to cardiovascular pathology associated with diabetes, including dysregulation of matrix metalloproteinases (MMPs). Quercetin (QCT) is a substance with preventive effects in treatment of cardiovascular diseases and diabetes. The aim of the present study was to explore effects of chronic QCT administration on changes in heart function in aged lean and obese Zucker Diabetic Fatty (ZDF) rats and that in association with MMPs. Signaling underlying effects of diabetes and QCT were also investigated. In the study, we used one-year-old lean and obese ZDF rats treated for 6 weeks with QCT. Results showed that obesity worsened heart function and this was associated with MMP-2 upregulation, MMP-28 downregulation, and inhibition of superoxide dismutases (SODs). Treatment with QCT did not modulate diabetes-induced changes in heart function and MMPs. However, QCT activated Akt kinase and reversed effects of diabetes on SODs inhibition. In conclusion, worsened heart function due to obesity involved changes in MMP-2 and MMP-28 and attenuation of antioxidant defense by SOD. QCT did not have positive effects on improvement of heart function or modulation of MMPs. Nevertheless, its application mediated activation of adaptive responses against oxidative stress through Akt kinase and prevention of diabetes-induced negative effects on antioxidant defense by SODs.     

Size and Fluorescence Properties of Algal Photosynthetic Antenna Proteins Estimated by Microscopy

Antenna proteins play a major role in the regulation of light-harvesting in photosynthesis. However, less is known about a possible link between their sizes (oligomerization state) and fluorescence intensity (number of photons emitted). Here, we used a microscopy-based method, Fluorescence Correlation Spectroscopy (FCS), to analyze different antenna proteins at the particle level. The direct comparison indicated that Chromera Light Harvesting (CLH) antenna particles (isolated from Chromera velia) behaved as the monomeric Light Harvesting Complex II (LHCII) (from higher plants), in terms of their radius (based on the diffusion time) and fluorescence yields. FCS data thus indicated a monomeric oligomerization state of algal CLH antenna (at our experimental conditions) that was later confirmed also by biochemical experiments. Additionally, our data provide a proof of concept that the FCS method is well suited to measure proteins sizes (oligomerization state) and fluorescence intensities (photon counts) of antenna proteins per single particle (monomers and oligomers). We proved that antenna monomers (CLH and LHCIIm) are more “quenched” than the corresponding trimers. The FCS measurement thus represents a useful experimental approach that allows studying the role of antenna oligomerization in the mechanism of photoprotection.     

Broad Specific Xyloglucan:Xyloglucosyl Transferases Are Formidable Players in the Re-Modelling of Plant Cell Wall Structures

Plant xyloglucan:xyloglucosyl transferases, known as xyloglucan endo-transglycosylases (XETs) are the key players that underlie plant cell wall dynamics and mechanics. These fundamental roles are central for the assembly and modifications of cell walls during embryogenesis, vegetative and reproductive growth, and adaptations to living environments under biotic and abiotic (environmental) stresses. XET enzymes (EC 2.4.1.207) have the β-sandwich architecture and the β-jelly-roll topology, and are classified in the glycoside hydrolase family 16 based on their evolutionary history. XET enzymes catalyse transglycosylation reactions with xyloglucan (XG)-derived and other than XG-derived donors and acceptors, and this poly-specificity originates from the structural plasticity and evolutionary diversification that has evolved through expansion and duplication. In phyletic groups, XETs form the gene families that are differentially expressed in organs and tissues in time- and space-dependent manners, and in response to environmental conditions. Here, we examine higher plant XET enzymes and dissect how their exclusively carbohydrate-linked transglycosylation catalytic function inter-connects complex plant cell wall components. Further, we discuss progress in technologies that advance the knowledge of plant cell walls and how this knowledge defines the roles of XETs. We construe that the broad specificity of the plant XETs underscores their roles in continuous cell wall restructuring and re-modelling.     

Synthetic Polyamine BPA‐C8 Inhibits TGF‐β1‐Mediated Conversion of Human Dermal Fibroblast to Myofibroblasts and Establishment of Galectin‐1‐Rich Extracellular Matrix in Vitro

Cancer‐associated fibroblasts (CAFs) play a role in the progression of malignant tumors. They are formed by conversion of fibroblasts to smooth muscle α‐actin‐positive (SMA‐positive) myofibroblasts. Polyamines are known to change the arrangement of the actin cytoskeleton by binding to the anionic actin. We tested the effect of the synthetic polyamine BPA‐C8 on the transition of human dermal fibroblasts to myofibroblasts induced either by TGF‐β1 alone or by TGF‐β1 together with adhesion/growth‐regulatory galectin‐1. Pre‐existing CAFs, myofibroblasts from pancreatitis, and rat smooth muscle cells were also exposed to BPA‐C8. BPA‐C8 impaired myofibroblast formation from activated fibroblasts, but it had no effect on cells already expressing SMA. BPA‐C8 also reduced the occurrence of an extracellular matrix around the activated fibroblasts. The reported data thus extend current insights into polyamine activity, adding interference with tumor progression to the tumor‐promoting processes warranting study.     

In situ co-adsorption of arsenic and iron/manganese ions on raw clays

The use of clays as effective arsenic sorbents has been strongly limited due to their low pH_ZPC and cation active behaviour in aqueous systems at pH > 3.5. A simple Fe/Al/Mn pre-treatment can significantly improve their sorption affinity to oxyanions, including arsenites and arsenates. The dynamics of arsenic adsorption from groundwater is also controlled by dissolved Fe/Mn ions, which behave as promoters of As adsorption, or competitors to adsorption sites. Low grade calcinated kaolin (MT) and bentonite (BT) were used as clay sorbents. Arsenic adsorption on raw clays without presence of Fe/Mn ions is very slow and limited. During co-adsorption the Fe/Mn ions and As oxyanions were adsorbed together onto a sorbent surface. Both Mn and Fe particles demonstrated a good sorption affinity to the clay surface, but only Fe particles supported As adsorption considerably (80% of As were removed in Fe/As system, while < 30% only in the Mn/As system). The kinetics of co-adsorption compared to the use of Fe/Mn pre-modified sorbents indicated a more dynamic process, while all mechanisms corresponded to the first order run (k ≈ 9.10^− 6- 1.10^− 4 s^− 1). Arsenic was strongly stabilized in pre-modified sorbents.